numpy v2 + py3.11 support

danmoser · Dec 2, 2024 · 5b754e0 · 5b754e0
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diff --git a/README.rst b/README.rst
@@ -22,6 +22,13 @@ I strongly suggest users to use the ``pip`` plataform:
 
     pip install pyhdust
 
+**pyhdust** dependencies are constantly evolving. If you face an installation problem, 
+check the `versioning page <https://pyhdust.readthedocs.io/alternative.html>`_. To install a specify version (for example, *1.5.12*):
+
+.. code:: bash
+
+    pip install "pyhdust==1.5.12"
+
 If your are not the root of the system, add the flag ``--user`` to the command above. Dependencies (as filters efficiency and stellar evolution models) are included in the subdirectories.
 
 .. warning::

diff --git a/docs/conf.py b/docs/conf.py
@@ -53,7 +53,7 @@
 
 # General information about the project.
 project = "Python tools for the BeACoN group"
-copyright = "2015-2021, D. Moser"
+copyright = "2015-2025, D. Moser"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/docs/index.rst b/docs/index.rst
@@ -4,7 +4,7 @@ Welcome to **pyhdust** documentation!
 =============================================================
 **Analysis tools for multi-technique astronomical data and** *hdust* **models**. About the *hdust* code, see Carciofi & Bjorkman (`2006 <http://adsabs.harvard.edu/abs/2006ApJ...639.1081C>`_, `2008 <http://adsabs.harvard.edu/abs/2008ApJ...684.1374C>`_).
 
-Pyhdust is currently at **version 1.5.12-1**. |Tests| 
+Pyhdust is currently at **version 1.6.0**. |Tests| 
 
 .. |Tests| image:: https://github.com/danmoser/pyhdust/actions/workflows/main.yaml/badge.svg
    :target: https://github.com/danmoser/pyhdust/actions/workflows/main.yaml
@@ -44,6 +44,13 @@ I strongly suggest users to use the ``pip`` plataform:
 
     pip install pyhdust
 
+**pyhdust** dependencies are constantly evolving. If you face an installation problem, 
+check the :doc:`versioning <versioning>` page. To install a specify version (for example, *1.5.12*):
+
+.. code:: bash
+
+    pip install "pyhdust==1.5.12"
+
 If your are not the root of the system, add the flag ``--user`` to the command above. Dependencies (as filters efficiency and stellar evolution models) are included in the subdirectories.
 
 .. warning::

diff --git a/docs/versioning.rst b/docs/versioning.rst
@@ -0,0 +1,31 @@
+Versioning
+=========================================
+Legacy versions
+------------------
+For *numpy < 2*, use *pyhdust < 1.6*.
+
+
+Version 1.6.0
+--------------
+**pyhdust** 1.6.0 was tested with the following modules:
+
+.. code::
+
+    astropy                       7.0.0
+    emcee                         3.1.6
+    ipython                       8.29.0
+    matplotlib                    3.9.2
+    numpy                         2.1.3
+    packaging                     24.2
+    pandas                        2.2.3
+    pip                           24.2
+    pyhdust                       1.6.0
+    python-dateutil               2.9.0.post0
+    scipy                         1.14.1
+    setuptools                    75.1.0
+    six                           1.16.0
+    Sphinx                        8.1.3
+    sphinx-rtd-theme              3.0.2
+    wget                          3.2
+    wheel                         0.44.0
+    xmltodict                     0.14.2
diff --git a/pyhdust/__init__.py b/pyhdust/__init__.py
@@ -38,7 +38,7 @@
 except ImportError:
     _warn.warn("# matplotlib and/or scipy module not installed!!")
 
-__version__ = "1.5.12-1"
+__version__ = "1.6.0"
 __release__ = "Stable"
 __author__ = "Daniel Moser"
 __email__ = "[email protected]"
@@ -2366,7 +2366,7 @@ def obs_ver(hmin, hnas, hmax, hpoe):
         else:
             if debug:
                 print(hmin, hnas, hmax, hpoe)
-            hnas = hpoe = _np.NaN
+            hnas = hpoe = _np.nan
         return (hnas, hpoe)
 
     # equinocio set 2011 (djsol)
@@ -2495,8 +2495,8 @@ def obs_ver(hmin, hnas, hmax, hpoe):
         if dt > 12:
             dt = dt - 24
         if dt < 3 / 4.0:
-            hnas = _np.NaN
-            hpoe = _np.NaN
+            hnas = _np.nan
+            hpoe = _np.nan
 
         # procura posicao nas efemerides (pef)
         if _os.path.exists("{0}refs/obs_ef.txt".format(hdtpath())):
@@ -2550,8 +2550,8 @@ def obs_ver(hmin, hnas, hmax, hpoe):
             fase_inc = ((djnas - T0) % per) / per
             fase_fim = ((djpoe - T0) % per) / per
         else:
-            fase_inc = _np.NaN
-            fase_fim = _np.NaN
+            fase_inc = _np.nan
+            fase_fim = _np.nan
 
         # tempos locais
         hlmin = hnas - hz

diff --git a/pyhdust/beatlas.py b/pyhdust/beatlas.py
@@ -802,7 +802,7 @@ def interpolBA(params, ctrlarr, lparams, minfo, models, param=True):
 
     | -params = from emcee minimization
     | -ctrlarr = the fixed value of M, ob(W), Z, H, sig, Rd, h, *n*, cos(i).
-    |            If it is not fixed, use np.NaN.
+    |            If it is not fixed, use np.nan.
     | -Parametric disk model default (`param` == True).
 
     This function always returns a valid result (i.e., extrapolations from the
@@ -823,7 +823,7 @@ def interpolBA(params, ctrlarr, lparams, minfo, models, param=True):
     parlims = _np.zeros((len(params), 2))
     j = 0
     for i in range(nq):
-        if ctrlarr[i] is _np.NaN:
+        if ctrlarr[i] is _np.nan:
             parlims[j] = [
                 _phc.find_nearest(lparams[i], params[j], bigger=False),
                 _phc.find_nearest(lparams[i], params[j], bigger=True),

diff --git a/pyhdust/fieldstars.py b/pyhdust/fieldstars.py
@@ -3188,7 +3188,7 @@ def run_emcee(sampler, p0):
             ),  #                            truths=[p_mcmc[0], l_mcmc[0]], \
             #                            extents=[(p_range[0],l_range[0]),(p_range[1],l_range[1])], \
             quantiles=[0.16075, 0.50, 0.83925],
-            labels=["$P_{max}\,($%$)$", "$\lambda_{max}\,(\mu m)$"],
+            labels=[r"$P_{max}\,($%$)$", r"$\lambda_{max}\,(\mu m)$"],
             verbose=False,
         )
         fig.savefig("{0}_correl.{1}".format(star, extens))
@@ -3199,7 +3199,7 @@ def run_emcee(sampler, p0):
             ),  #                            truths=[p_mcmc[0], l_mcmc[0]], \
             #                            extents=[(p_range[0],l_range[0]),(p_range[1],l_range[1])], \
             quantiles=[0.16075, 0.50, 0.83925],
-            labels=["$P_{max}\,($%$)$", "$\lambda_{max}\,(\mu m)$"],
+            labels=[r"$P_{max}\,($%$)$", r"$\lambda_{max}\,(\mu m)$"],
             verbose=False,
         )
         fig1.show()
@@ -3379,7 +3379,7 @@ def run_emcee(sampler, p0):
                 ),  #                                 truths=[p_mcmc[0], l_mcmc[0]], \
                 #                                 extents=[(p_range[0],l_range[0]),(p_range[1],l_range[1])], \
                 quantiles=[0.16075, 0.50, 0.83925],
-                labels=["$P_{max}\,($%$)$", "$\lambda_{max}\,(\mu m)$"],
+                labels=[r"$P_{max}\,($%$)$", r"$\lambda_{max}\,(\mu m)$"],
                 verbose=False,
             )
             fig.savefig("{0}_correl_cut.{1}".format(star, extens))
@@ -3401,7 +3401,7 @@ def plot_samples_hist(sampler):
         Plot two figures with the histograms
         """
         samples = [sampler.flatchain[:, i] for i in (0, 1)]
-        par = ["$P_{max}$", "$\lambda_{max}$"]
+        par = ["$P_{max}$", r"$\lambda_{max}$"]
 
         fig = []
         for i, sample in enumerate(samples):
@@ -3426,7 +3426,7 @@ def plot_conv(sampler, param):
         axes[1].plot(sampler.chain[:, :, 1].T, color="k", alpha=0.4)
         axes[1].yaxis.set_major_locator(MaxNLocator(5))
         axes[1].axhline(param[1], color="#888888", lw=2)
-        axes[1].set_ylabel("$\lambda_{max}$")
+        axes[1].set_ylabel(r"$\lambda_{max}$")
         axes[1].set_xlabel("Step number")
 
         fig.tight_layout(h_pad=0.0)

diff --git a/pyhdust/interftools.py b/pyhdust/interftools.py
@@ -82,7 +82,7 @@ def log_transform(im):
                 _np.log(imax) - _np.log(imin)
             )
             idx = _np.where(im == 0)
-            im[idx] = _np.NaN
+            im[idx] = _np.nan
             return im
     except:
         _warn.warn("# Warning! Wrong input at log_transform !!!")
@@ -865,7 +865,7 @@ def add_model(self, imgs, rpx, PAdisk=90, modid=None, lbm=None):
                 )
                 tlist.extend([v**2])
             self.v2 = _np.array(tlist)
-            self.v2e = _np.zeros(_np.shape(tlist)) * _np.NaN
+            self.v2e = _np.zeros(_np.shape(tlist)) * _np.nan
             #
             tlist = []
             for i in range(len(self.t3B1)):
@@ -881,7 +881,7 @@ def add_model(self, imgs, rpx, PAdisk=90, modid=None, lbm=None):
                 )
                 tlist.extend([p])
             self.t3p = _np.array(tlist)
-            self.t3pe = _np.zeros(_np.shape(tlist)) * _np.NaN
+            self.t3pe = _np.zeros(_np.shape(tlist)) * _np.nan
         #
         elif self.oitype.upper().startswith("AMB"):
             if lbm is not None:
@@ -902,9 +902,9 @@ def add_model(self, imgs, rpx, PAdisk=90, modid=None, lbm=None):
                 tlist_v.extend([v])
                 tlist_vp.extend([vp])
             self.v = _np.array(tlist_v)
-            self.ve = _np.zeros(_np.shape(tlist_v)) * _np.NaN
+            self.ve = _np.zeros(_np.shape(tlist_v)) * _np.nan
             self.vp = _np.array(tlist_vp)
-            self.vpe = _np.zeros(_np.shape(tlist_vp)) * _np.NaN
+            self.vpe = _np.zeros(_np.shape(tlist_vp)) * _np.nan
         return
 
 

diff --git a/pyhdust/phc.py b/pyhdust/phc.py
@@ -121,7 +121,7 @@ def find_nearest_pt(x0, y0, x, y, z, case=1):
             _np.average(d[idx]),
         )
     else:
-        return _np.NaN, _np.NaN, _np.NaN, _np.NaN
+        return _np.nan, _np.nan, _np.nan, _np.nan
 
 
 def baricent_calc(x0, y0, x, y, z, fullrange=False):
@@ -171,7 +171,7 @@ def baricent_calc(x0, y0, x, y, z, fullrange=False):
         ds = _np.array([d1, d2, d3, d4])[idx][:3]
         return _np.sum(zs / ds) / _np.sum(1 / ds)
     else:
-        return _np.NaN
+        return _np.nan
 
 
 def baricent_map(x, y, z, res=100, fullrange=False, xfact=1.0, yfact=1.0):
@@ -426,9 +426,9 @@ def interLinND(X, X0, X1, Fx, disablelog=False):
     F = 0
     for prod in _product(*DX):
         if disablelog:
-            F += Fx[i] * _np.product(prod)
+            F += Fx[i] * _np.prod(prod)
         else:
-            F += _np.log(Fx[i]) * _np.product(prod)
+            F += _np.log(Fx[i]) * _np.prod(prod)
         i += 1
     #
     if not disablelog:
@@ -812,7 +812,7 @@ def fltTxtOccur(s, lines, n=1, seq=1, after=True, asstr=False):
         occur = [x[x.find(s) + len(s) :] for x in lines if x.find(s) > -1]
     else:
         occur = [x for x in lines if x.find(s) > -1]
-    out = _np.NaN
+    out = _np.nan
     if len(occur) >= n:
         occur = occur[n - 1]
         out = _re.findall(fltregex, occur)[seq - 1]
@@ -1846,8 +1846,8 @@ def gbf(T, lbd):
     else:
         i = _np.where(
             vals[:, 0] == find_nearest(vals[:, 0], _np.log10(T), bigger=False)
-        )[0]
-        # print i, vals[i,0]
+        )[0][0]
+        # print(i, vals, type(i), type(vals))
         g0 = interLinND(
             [_np.log10(T)], [vals[i, 0]], [vals[i + 1, 0]], vals[i : i + 2, 1]
         )

diff --git a/pyhdust/poltools.py b/pyhdust/poltools.py
@@ -43,7 +43,7 @@ def eprint(*args, **kwargs):
     import matplotlib.pyplot as _plt
     from matplotlib.transforms import offset_copy as _offset_copy
     from scipy.optimize import curve_fit as _curve_fit
-    from scipy.integrate import simps as _simps
+    from scipy.integrate import simpson as _simps
     from scipy.interpolate import interp1d as _interp1d
     import matplotlib as _mpl
 

diff --git a/pyhdust/releases.py b/pyhdust/releases.py
@@ -4,6 +4,10 @@
 
 History
 ============
+v.1.6.0 @ 2024-12-02
+---------------------
+- numpy v2 + Py3.11+ support 
+
 v1.5.12 @ 2024-04-10
 ---------------------
 - oifits compatible w/ Python3.8+

diff --git a/pyhdust/rotstars.py b/pyhdust/rotstars.py
@@ -510,7 +510,7 @@ def sigma4b_cranmer(M, wfrac):
     # H = 0.3 core
     # For ob=1.10, i.e., one *CAN'T* apply 4*pi*R^2...
     # SpType Tpole    Teff    Mass   Rp    Lum
-    ["B0.0", _np.NaN, _np.NaN, _np.NaN, _np.NaN, _np.NaN],
+    ["B0.0", _np.nan, _np.nan, _np.nan, _np.nan, _np.nan],
     ["B0.5", 28905.8, 26765.7, 14.6, 7.50, 31183.26],
     ["B1.0", 26945.8, 24950.9, 12.5, 6.82, 19471.38],
     ["B1.5", 25085.2, 23228.2, 10.8, 6.23, 12204.70],
@@ -540,7 +540,7 @@ def sigma4b_cranmer(M, wfrac):
     ["B6.0", 14300.3, 13241.6, 04.2, 3.72, 00459.55],
     ["B7.0", 13329.9, 12343.0, 03.8, 3.55, 00315.96],
     ["B8.0", 12307.1, 11395.9, 03.4, 3.37, 00206.89],
-    ["B9.0", _np.NaN, _np.NaN, _np.NaN, _np.NaN, _np.NaN],
+    ["B9.0", _np.nan, _np.nan, _np.nan, _np.nan, _np.nan],
 ]